Objective: Stress fractures (SF), menstrual dysfunction (MD), and eating disorders (ED) in young athletes are important issues. We conducted this study to determine the frequency of SF, MD, and ED experienced by high school track and field athletes in Japan and to understand the factors associated with them. Materials and Methods: A cross-sectional study of 1199 high level high school track and field athletes (608 males and 591 females) who participated in a selective training camp held by the Japan Association of Athletics Federations. Results: Approximately one in four male and female athletes self-reported SF. Moreover, we identified the length of the practice time per week and the event (sprinting, middle-distance, jumping, and combined) as relevant factors. Approximately one in three female athletes self-reported MD history, with those participating in long-distance events experiencing it significantly more frequently than those participants in sprinting, throwing, and jumping events. Furthermore, we identified ED history and long-distance events as MD history-related factors. ED history was self-reported at low frequency without gender difference, and long-distance was significantly more frequently reported than sprinting and jumping. Conclusions: About a quarter of Japanese high school track and field athletes experience SF, and about a third of the females experience MD. The association of these with athletic events, training time, and ED should be considered.